Synonymous Codon Usages as an Evolutionary Dynamic for Chlamydiaceae.

Ping Liu,Zhaocai Li,Jizhang Zhou,Wen Hu,Youjun Shang,Xiaoan Cao

doi:10.3390/ijms19124010

Abstract

The family of Chlamydiaceae contains a group of obligate intracellular bacteria that can infect a wide range of hosts. The evolutionary trend of members in this family is a hot topic, which benefits our understanding of the cross-infection of these pathogens. In this study, 14 whole genomes of 12 Chlamydia species were used to investigate the nucleotide, codon, and amino acid usage bias by synonymous codon usage value and information entropy method. The results showed that all the studied Chlamydia spp. had A/T rich genes with over-represented A or T at the third positions and G or C under-represented at these positions, suggesting that nucleotide usages influenced synonymous codon usages. The overall codon usage trend from synonymous codon usage variations divides the Chlamydia spp. into four separate clusters, while amino acid usage divides the Chlamydia spp. into two clusters with some exceptions, which reflected the genetic diversity of the Chlamydiaceae family members. The overall codon usage pattern represented by the effective number of codons (ENC) was significantly positively correlated to gene GC3 content. A negative correlation exists between ENC and the codon adaptation index for some Chlamydia species. These results suggested that mutation pressure caused by nucleotide composition constraint played an important role in shaping synonymous codon usage patterns. Furthermore, codon usage of T3ss and Pmps gene families adapted to that of the corresponding genome. Taken together, analyses help our understanding of evolutionary interactions between nucleotide, synonymous codon, and amino acid usages in genes of Chlamydiaceae family members.

Highlights

Chlamydia spp. are a group of obligate intracellular bacteria that are widely distributed throughout the world, causing a variety of diseases in humans and animals [1]
We gave an evolutionary insight into the relationship between nucleotide usages and codon usages in genomes of Chlamydiaceae family members, by means of information entropy, Relative Synonymous Codon Usage (RSCU), effective number of codons (ENC), codon adaptation index (CAI) and a similarity index of codon usage adaptation
Mutation pressure derived from nucleotide usages was identified as the dominant evolutionary dynamic in genomes of Chlamydia spp., other evolutionary dynamics, such as natural selection, influenced codon usage patterns to modify the evolutionary trends of Chlamydia spp

Summary

Introduction

Chlamydia spp. are a group of obligate intracellular bacteria that are widely distributed throughout the world, causing a variety of diseases in humans and animals [1]. 12 species have been identified in the single genus of the family Chlamydiaceae: C. trachomatis, C. pneumoniae, C. muridarum, C. suis, C. psittaci, C. pecorum, C. abortus, C. felis, C. caviae, C. avium, C. gallinacea, and C. ibidis [2,3]. Among these species, C. trachomatis and C. pneumonia mainly cause diseases in humans, while other species often cause animal diseases and most have zoonotic potential [4]. C. trachomatis infects the ocular and genital mucosa It is the leading cause of infectious preventable blindness in developing countries and contributes to the most prevalent bacterial sexually transmitted diseases (STDs) throughout the world [5,6]. C. avium, C. gallinacea, and C. ibidis are newly identified chlamydial species from birds with unclear pathogenicity [3,12,13]

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Results

Conclusion